def test09getAtomsFromSegment2(self):
pdbFileName = "../../pdbs/2J9N.pdb"
segmentFileName = "../../pdbs/2J9N_A_101_102.pdb"
chain = " A "
start = 101
stop = 102
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segment =[]
#chain, start, stop, startInsertion, stopInsertion, startOder, stopOrder, model=0, onlyBackbone=False):
segment = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segment is not None
file = open(segmentFileName,"w")
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.write("%s\n" % ("END"+77*" ",))
file.close()
def extractDomains(self, model=0, onlyBackbone=False, verbose=False):
"""1.-query the database to know every pair(pdbID, domainID)
2.-for each domain of the family contained in the pdb, load its segments.
3.-for each domain serialize it with the name domain.pdb
"""
(db, cursor) = queryCDDF.setUpDB(self.__host, self.__user, self.__passwd, self.__db)
self.PDB_Domains = queryCDDF.loadCATHfamilyDomains(self.cathcode, cursor)
for (pdbID, domain) in self.PDB_Domains:
validDomain = True
segments = queryCDDF.loadSegments(domain, cursor)
for segment in segments:
if segment[1] != -1:
self.validSegments.append((pdbID, domain, segment))
else:
self.notValidSegments.append((pdbID, domain, segment))
validDomain = False
if validDomain:
try:
pdb = PDB(self.__composeLocalFileName(self.workingDirectory, pdbID, ".pdb"))
pdb.load_atoms_hetams()
except IOError:
print "%s does not exist" %(self.__composeLocalFileName(self.workingDirectory, pdbID, ".pdb"),)
else:
pdb.serializeSegments(segments, self.__composeLocalFileName(self.workingDirectory, domain, ".pdb"), model, onlyBackbone)
if verbose:
print ("%s domain extracted" % (domain,))
queryCDDF.tearDownDB(db, cursor)
def test08highestOccupancyLevel(self):
rawAtom = "ATOM 661 CA AMET A 101 16.070 45.718 27.607 0.20 7.83 C "
anAtom = Atom(rawAtom)
pdbFileName = "../../pdbs/multipleLocations.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
assert 'A' == anAtom.alternateLocation()
print "%c" % (pdb.getHighestOccupancyLocation(anAtom),)
assert 'B' == pdb.getHighestOccupancyLocation(anAtom)
def test17getFirstResidue(self):
pdblistFileName = "../../pdbs/pdbFileList.lst"
workingDirectory = "../../pdbs/"
pdListFile = open(pdblistFileName,"r")
for pdbFileName in pdListFile:
pdb = PDB(workingDirectory+pdbFileName.split()[0])
pdb.load_atoms_hetams()
firstResidue = pdb.getFirstResidue()
print ("%s = (%d % c) \n" % (pdbFileName,firstResidue[0],firstResidue[1]))
def test20sphereRadius(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
(cm, radius) = pdb.sphereRadius()
print ("radius %f \n"%(radius,))
sb = []
sb.extend(rjust("%.3f" % cm[0],8))
sb.extend(rjust("%.3f" % cm[1],8))
sb.extend(rjust("%.3f" % cm[2],8))
print ("%s\n", join(sb,''))
def test21getCAlphaFromResidue(self):
pdbFileName = "../../pdbs/1a0hA02.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
pdb.loadIntSeqRes()
atom = pdb.getCAlphaFromResidue(0)
assert atom.toString() == "ATOM 2 CA ASP A 253 78.545 46.395 3.454 1.00 61.74 C "
atom = pdb.getCAlphaFromResidue(12)
assert atom.toString() == "ATOM 89 CA ASP A 264A 63.823 29.490 -10.700 1.00 86.06 C "
def atest15Fasta2(self):
pdb1avgL00 = "../../pdbs/1avgL00.pdb"
pdb1bbrJ00 = "../../pdbs/1bbrJ00.pdb"
fasta1avgL00 = "../../pdbs/1avgL00.fasta"
fasta1bbrJ00 = "../../pdbs/1bbrJ00.fasta"
Pdb1avgL00 = PDB(pdb1avgL00)
Pdb1bbrJ00 = PDB(pdb1bbrJ00)
Pdb1avgL00.load_atoms_hetams()
Pdb1bbrJ00.load_atoms_hetams()
Pdb1avgL00.fasta(fasta1avgL00)
Pdb1bbrJ00.fasta(fasta1bbrJ00)
def test05getAtomsFromSegment(self):
pdbFileName = "../../pdbs/1A00.pdb"
chain = " A "
start = 1
stop = 141
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segments is not None
for (lineNumber, atom) in segments.items():
print "[%d] = %s" %(lineNumber, atom.toString())
def test03Transform(self):
self.pdb = PDB(PDBTestCase.pdbFileName)
self.pdb.load_atoms_hetams()
center = matrix([0, 0, 0]).T
shift = matrix([1, 1, 1]).T
rotationMatrix = rotationMatrices.XYZ(radians(90), radians(90), radians(90))
self.pdb.chimera_transform(center, rotationMatrix, shift)
self.pdb.serialize("../../pdbs/transformed.pdb")
self.pdb = None
def test19getAtomsFromResidue(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
pdb.loadIntSeqRes()
atoms = pdb.getAtomsFromResidue(0)
assert len(atoms) > 0
assert len(atoms) == 7
for atom in atoms:
print ("%s\n" % (atom.toString(),))
def test13getAtomsFromDomain(self):
pdbFileName = "../../pdbs/1JMO.pdb"
domainFileName = "../../pdbs/1jmoL00.pdb"
file = open(domainFileName, "w")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments =[]
segments.append(('L', 1, 14,'B','M'))
#segments.append(('A',385,401))
#segments.append(('A',443,505))
domains = pdb.getAtomsFromDomain(segments)
for segment in domains:
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.close()
def test04Itk_ops(self):
self.pdb = PDB(PDBTestCase.pdbFileName)
self.pdb.load_atoms_hetams()
rotationMatrix = matrix ([[0.742755, -0.0816224, 0.664569], [0.286523, 0.93582, -0.205295], [-0.605161, 0.342898, 0.718472]])
shift = matrix([-6.01415, 4.92925, 16.1776]).T
"""shift = matrix([2,5,4]).T"""
target_first_voxel = matrix([58, -14, 28]).T
model_first_voxel = matrix([60, -14, 28]).T
self.pdb.itk_transform(rotationMatrix, shift)
print "completed"
self.pdb.serialize("../../pdbs/1jlvC1.pdb")
self.pdb = None
def test16loadResidues(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
assert len(pdb.residues) > 0
def test01RASH(self):
queryFileName = "../../pdbs/1cf3A03.pdb"
pdb = PDB(queryFileName)
pdb.load_atoms_hetams()
center = matrix([42.639, 21.304, 46.057]).T
shift = matrix([15.155, -0.310, -36.823]).T
rotationMatrix = matrix ([[-0.030, 0.982, 0.186], [-0.999, -0.036, 0.029], [0.035, -0.185, 0.982]])
pdb.ash_transform(center, rotationMatrix, shift)
pdb.serialize("../../pdbs/1cf3A03_RT.pdb")
templateFileName = "../../pdbs/1gpeA03.pdb"
pdb = PDB(templateFileName)
pdb.load_atoms_hetams()
center = matrix([42.639, 21.304, 46.057]).T
shift = matrix([15.155, -0.310, -36.823]).T
rotationMatrix = matrix ([[-0.030, 0.982, 0.186], [-0.999, -0.036, 0.029], [0.035, -0.185, 0.982]])
pdb.ash_transform(center, rotationMatrix, shift)
pdb.serialize("../../pdbs/1gpeA03_RT.pdb")
class PDBTestCase(unittest.TestCase):
pdbFileName = "../../pdbs/1CBO.pdb"
def test01RASH(self):
queryFileName = "../../pdbs/1cf3A03.pdb"
pdb = PDB(queryFileName)
pdb.load_atoms_hetams()
center = matrix([42.639, 21.304, 46.057]).T
shift = matrix([15.155, -0.310, -36.823]).T
rotationMatrix = matrix ([[-0.030, 0.982, 0.186], [-0.999, -0.036, 0.029], [0.035, -0.185, 0.982]])
pdb.ash_transform(center, rotationMatrix, shift)
pdb.serialize("../../pdbs/1cf3A03_RT.pdb")
templateFileName = "../../pdbs/1gpeA03.pdb"
pdb = PDB(templateFileName)
pdb.load_atoms_hetams()
center = matrix([42.639, 21.304, 46.057]).T
shift = matrix([15.155, -0.310, -36.823]).T
rotationMatrix = matrix ([[-0.030, 0.982, 0.186], [-0.999, -0.036, 0.029], [0.035, -0.185, 0.982]])
pdb.ash_transform(center, rotationMatrix, shift)
pdb.serialize("../../pdbs/1gpeA03_RT.pdb")
def test02BasicOperations(self):
pdbFileName = "../../pdbs/1.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
x_shift = matrix([10, 0, 0]).T
y_shift = matrix([0, 10, 0]).T
z_shift = matrix([0, 0, 10]).T
pdb.shift(x_shift);
pdb.serialize("../../pdbs/x_shift.pdb")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.shift(y_shift)
pdb.serialize("../../pdbs/y_shift.pdb")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.shift(z_shift)
pdb.serialize("../../pdbs/z_shift.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.XYZ(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_xyz45_45_45.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.ZXY(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_zxy45_45_45.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.YXZ(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_yxz45_45_45.pdb")
def test03Transform(self):
self.pdb = PDB(PDBTestCase.pdbFileName)
self.pdb.load_atoms_hetams()
center = matrix([0, 0, 0]).T
shift = matrix([1, 1, 1]).T
rotationMatrix = rotationMatrices.XYZ(radians(90), radians(90), radians(90))
self.pdb.chimera_transform(center, rotationMatrix, shift)
self.pdb.serialize("../../pdbs/transformed.pdb")
self.pdb = None
def test04Itk_ops(self):
self.pdb = PDB(PDBTestCase.pdbFileName)
self.pdb.load_atoms_hetams()
rotationMatrix = matrix ([[0.742755, -0.0816224, 0.664569], [0.286523, 0.93582, -0.205295], [-0.605161, 0.342898, 0.718472]])
shift = matrix([-6.01415, 4.92925, 16.1776]).T
"""shift = matrix([2,5,4]).T"""
target_first_voxel = matrix([58, -14, 28]).T
model_first_voxel = matrix([60, -14, 28]).T
self.pdb.itk_transform(rotationMatrix, shift)
print "completed"
self.pdb.serialize("../../pdbs/1jlvC1.pdb")
self.pdb = None
def test05getAtomsFromSegment(self):
pdbFileName = "../../pdbs/1A00.pdb"
chain = " A "
start = 1
stop = 141
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segments is not None
for (lineNumber, atom) in segments.items():
print "[%d] = %s" %(lineNumber, atom.toString())
def test09getAtomsFromSegment2(self):
pdbFileName = "../../pdbs/2J9N.pdb"
segmentFileName = "../../pdbs/2J9N_A_101_102.pdb"
chain = " A "
start = 101
stop = 102
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segment =[]
#chain, start, stop, startInsertion, stopInsertion, startOder, stopOrder, model=0, onlyBackbone=False):
segment = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segment is not None
file = open(segmentFileName,"w")
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.write("%s\n" % ("END"+77*" ",))
file.close()
def test06getAtomsFromDomain(self):
pdbFileName = "../../pdbs/1CBO.pdb"
domainFileName = "../../pdbs/1cboA01.pdb"
file = open(domainFileName, "w")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments =[]
segments.append(('A', 9, 11,'',''))
#segments.append(('A',385,401))
#segments.append(('A',443,505))
domains = pdb.getAtomsFromDomain(segments)
for segment in domains:
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.close()
def test13getAtomsFromDomain(self):
pdbFileName = "../../pdbs/1JMO.pdb"
domainFileName = "../../pdbs/1jmoL00.pdb"
file = open(domainFileName, "w")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments =[]
segments.append(('L', 1, 14,'B','M'))
#segments.append(('A',385,401))
#segments.append(('A',443,505))
domains = pdb.getAtomsFromDomain(segments)
for segment in domains:
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.close()
def test07CenterOfMass(self):
pdbFileName = "../../pdbs/1cboA01.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
print "center of mass: %f %f %f\n" % (pdb.centerOfMass()[0], pdb.centerOfMass()[1], pdb.centerOfMass()[2])
def test08highestOccupancyLevel(self):
rawAtom = "ATOM 661 CA AMET A 101 16.070 45.718 27.607 0.20 7.83 C "
anAtom = Atom(rawAtom)
pdbFileName = "../../pdbs/multipleLocations.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
assert 'A' == anAtom.alternateLocation()
print "%c" % (pdb.getHighestOccupancyLocation(anAtom),)
assert 'B' == pdb.getHighestOccupancyLocation(anAtom)
def test10orderOfInsertions(self):
pdbFileName = "../../pdbs/1JMO.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
assert pdb.orderOfInsertions(1) == False
assert pdb.orderOfInsertions(14) == True
def test14Fasta(self):
pdbFileName = "../../pdbs/1JMO.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
fastaFileName = "../../pdbs/1JMO.fasta"
pdb.fasta(fastaFileName)
def atest15Fasta2(self):
pdb1avgL00 = "../../pdbs/1avgL00.pdb"
pdb1bbrJ00 = "../../pdbs/1bbrJ00.pdb"
fasta1avgL00 = "../../pdbs/1avgL00.fasta"
fasta1bbrJ00 = "../../pdbs/1bbrJ00.fasta"
Pdb1avgL00 = PDB(pdb1avgL00)
Pdb1bbrJ00 = PDB(pdb1bbrJ00)
Pdb1avgL00.load_atoms_hetams()
Pdb1bbrJ00.load_atoms_hetams()
Pdb1avgL00.fasta(fasta1avgL00)
Pdb1bbrJ00.fasta(fasta1bbrJ00)
def test16loadResidues(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
assert len(pdb.residues) > 0
def test17getFirstResidue(self):
pdblistFileName = "../../pdbs/pdbFileList.lst"
workingDirectory = "../../pdbs/"
pdListFile = open(pdblistFileName,"r")
for pdbFileName in pdListFile:
pdb = PDB(workingDirectory+pdbFileName.split()[0])
pdb.load_atoms_hetams()
firstResidue = pdb.getFirstResidue()
print ("%s = (%d % c) \n" % (pdbFileName,firstResidue[0],firstResidue[1]))
def test18getIntSeqRes(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdbFileName2 = "../../pdbs/1a0hA02.pdb"
pdb = PDB(pdbFileName)
pdb2 = PDB(pdbFileName2)
pdb.load_atoms_hetams()
pdb2.load_atoms_hetams()
pdb.loadResidues()
pdb2.loadResidues()
pdb.loadIntSeqRes()
pdb2.loadIntSeqRes()
assert pdb.getIntSeqRes(0) == (1,'U')
assert pdb.getIntSeqRes(1) == (1,'T')
assert pdb2.getIntSeqRes(0) == (253,' ')
def test19getAtomsFromResidue(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
pdb.loadIntSeqRes()
atoms = pdb.getAtomsFromResidue(0)
assert len(atoms) > 0
assert len(atoms) == 7
for atom in atoms:
print ("%s\n" % (atom.toString(),))
# print("%.3f %.3f %.3f" % (atom[0,0],atom[1,0], atom[2,0]))
def test20sphereRadius(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
(cm, radius) = pdb.sphereRadius()
print ("radius %f \n"%(radius,))
sb = []
sb.extend(rjust("%.3f" % cm[0],8))
sb.extend(rjust("%.3f" % cm[1],8))
sb.extend(rjust("%.3f" % cm[2],8))
print ("%s\n", join(sb,''))
def test21getCAlphaFromResidue(self):
pdbFileName = "../../pdbs/1a0hA02.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.loadResidues()
pdb.loadIntSeqRes()
atom = pdb.getCAlphaFromResidue(0)
assert atom.toString() == "ATOM 2 CA ASP A 253 78.545 46.395 3.454 1.00 61.74 C "
atom = pdb.getCAlphaFromResidue(12)
assert atom.toString() == "ATOM 89 CA ASP A 264A 63.823 29.490 -10.700 1.00 86.06 C "
def test02BasicOperations(self):
pdbFileName = "../../pdbs/1.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
x_shift = matrix([10, 0, 0]).T
y_shift = matrix([0, 10, 0]).T
z_shift = matrix([0, 0, 10]).T
pdb.shift(x_shift);
pdb.serialize("../../pdbs/x_shift.pdb")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.shift(y_shift)
pdb.serialize("../../pdbs/y_shift.pdb")
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.shift(z_shift)
pdb.serialize("../../pdbs/z_shift.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.XYZ(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_xyz45_45_45.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.ZXY(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_zxy45_45_45.pdb")
alpha = radians(45)
rotationMatrix = rotationMatrices.YXZ(alpha, alpha, alpha)
center = matrix([0, 0, 0]).T
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
pdb.rotate(rotationMatrix, center)
pdb.serialize("../../pdbs/R_yxz45_45_45.pdb")
def test07CenterOfMass(self):
pdbFileName = "../../pdbs/1cboA01.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
print "center of mass: %f %f %f\n" % (pdb.centerOfMass()[0], pdb.centerOfMass()[1], pdb.centerOfMass()[2])
def test10orderOfInsertions(self):
pdbFileName = "../../pdbs/1JMO.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
assert pdb.orderOfInsertions(1) == False
assert pdb.orderOfInsertions(14) == True
def test14Fasta(self):
pdbFileName = "../../pdbs/1JMO.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
fastaFileName = "../../pdbs/1JMO.fasta"
pdb.fasta(fastaFileName)
def test18getIntSeqRes(self):
pdbFileName = "../../pdbs/1tbqL00.pdb"
pdbFileName2 = "../../pdbs/1a0hA02.pdb"
pdb = PDB(pdbFileName)
pdb2 = PDB(pdbFileName2)
pdb.load_atoms_hetams()
pdb2.load_atoms_hetams()
pdb.loadResidues()
pdb2.loadResidues()
pdb.loadIntSeqRes()
pdb2.loadIntSeqRes()
assert pdb.getIntSeqRes(0) == (1,'U')
assert pdb.getIntSeqRes(1) == (1,'T')
assert pdb2.getIntSeqRes(0) == (253,' ')